From 1e42cfa09e948aea26d5e7c4c164a1df7617bee0 Mon Sep 17 00:00:00 2001
From: j2blake <jeb228@cornell.edu>
Date: Mon, 8 Dec 2014 10:54:26 -0500
Subject: [PATCH] VIVO-778 Refactor the connections to the TBox reasoner.

Replace PelletListener with a TBoxReasonerModule in the Application.
   The reasoner will be accessible only through here, not as a context attribute or through the WebappDaoFactory.
Split out the initialization of the TBox reasoner from SimpleReasonerSetup.
Break out the filtering of TBox changes into a ConfiguredReasonerListener.
Refactor the threading logic into a BasicTBoxReasonerDriver.
   Add a factory for creating VitroBackgroundThreads in an Executor.
Isolate the actual reasoner into a TBoxReasoner implementation. In this case, PelletTBoxReasoner.
Combine the consistency flag, error flag, explanation, and running status into one TBoxReasonerStatus object.
---
 config/applicationSetup.n3                    | 31 +++++++++++--------
 .../WEB-INF/resources/startup_listeners.txt   |  1 +
 2 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/config/applicationSetup.n3 b/config/applicationSetup.n3
index 8f7ccf8e..46ee736c 100644
--- a/config/applicationSetup.n3
+++ b/config/applicationSetup.n3
@@ -3,33 +3,38 @@
 :application 
     a   <java:edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl> ,
         <java:edu.cornell.mannlib.vitro.webapp.modules.Application> ;
-    :hasSearchEngine              :searchEngineWrapper ;
-    :hasImageProcessor            :imageProcessor ;
-    :hasFileStorage               :fileStorage ;
-    :hasContentTripleSource       :contentTripleSource ;
-    :hasConfigurationTripleSource :configurationTripleSource .
+    :hasSearchEngine              :instrumentedSearchEngineWrapper ;
+    :hasImageProcessor            :jaiImageProcessor ;
+    :hasFileStorage               :ptiFileStorage ;
+    :hasContentTripleSource       :sdbContentTripleSource ;
+    :hasConfigurationTripleSource :tdbConfigurationTripleSource ;
+    :hasTBoxReasonerModule        :pelletTBoxReasonerModule .
 
-:imageProcessor 
+:jaiImageProcessor 
     a   <java:edu.cornell.mannlib.vitro.webapp.imageprocessor.jai.JaiImageProcessor> ,
         <java:edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor> .
 
-:fileStorage 
+:ptiFileStorage 
     a   <java:edu.cornell.mannlib.vitro.webapp.filestorage.impl.FileStorageImplWrapper> ,
         <java:edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage> .
                
-:searchEngineWrapper 
+:instrumentedSearchEngineWrapper 
     a   <java:edu.cornell.mannlib.vitro.webapp.searchengine.InstrumentedSearchEngineWrapper> , 
         <java:edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine> ;
-    :wraps :searchEngine .
+    :wraps :solrSearchEngine .
 
-:searchEngine
+:solrSearchEngine
     a   <java:edu.cornell.mannlib.vitro.webapp.searchengine.solr.SolrSearchEngine> ,
         <java:edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine> .
 
-:contentTripleSource
+:sdbContentTripleSource
     a   <java:edu.cornell.mannlib.vitro.webapp.triplesource.impl.sdb.ContentTripleSourceSDB> ,
         <java:edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ContentTripleSource> .
 
-:configurationTripleSource
+:tdbConfigurationTripleSource
     a   <java:edu.cornell.mannlib.vitro.webapp.triplesource.impl.tdb.ConfigurationTripleSourceTDB> ,
-        <java:edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ConfigurationTripleSource> .
\ No newline at end of file
+        <java:edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ConfigurationTripleSource> .
+        
+:pelletTBoxReasonerModule
+    a   <java:edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.pellet.PelletTBoxReasonerModule> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.tboxreasoner.TBoxReasonerModule> .
\ No newline at end of file
diff --git a/productMods/WEB-INF/resources/startup_listeners.txt b/productMods/WEB-INF/resources/startup_listeners.txt
index 9514f2bf..0e84a98b 100644
--- a/productMods/WEB-INF/resources/startup_listeners.txt
+++ b/productMods/WEB-INF/resources/startup_listeners.txt
@@ -37,6 +37,7 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup
 # Invokes process to perform updates to align with ontology changes if needed -->
 edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase
 
+edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl$ReasonersSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup
 
 # Must run after JenaDataSourceSetup